Japan has executed three inmates convicted of murder in its first executions since the new Government took office in December.

Kaoru Kobayashi, 44, abducted, assaulted and killed a seven-year-old girl in 2004, and sent a photograph of her body to her mother.

Masahiro Kanagawa, 29, killed one man and injured seven other people in a knifing spree outside a shopping mall in a Tokyo suburb in 2008; he also murdered another man in a separate incident the same year.

The third man hanged was Keiki Muto, 62, who strangled a bar owner for money in 2002.

"I ordered the executions after giving careful consideration to the matter," Justice Minister Sadakazu Tanigaki said as he confirmed they took place early on Thursday morning.

"These were extremely cruel cases in which victims were deprived of their precious lives for very selfish reasons."

The executions were Japan's first since two death-row inmates were hanged in September under a centre-left Democratic Party of Japan Government.

Japan did not execute any condemned inmates in 2011, the first full year in nearly two decades without an execution amid muted debate on the rights and wrongs of a policy that has wide public support.

But in March last year, Tokyo resumed its use of capital punishment with an unapologetic Government minister signing death warrants for three multiple murderers.

Apart from the US, Japan is the only major industrialised democracy to carry out capital punishment, a practice that has led to repeated protests from European governments and human rights groups.

International advocacy groups say the system is cruel because death row inmates can wait for their executions for many years in solitary confinement and are only told of their impending death a few hours ahead of time.